Discovery of type II polyketide synthase-like enzymes for the biosynthesis of cispentacin.

Type II polyketide synthases (PKSs) normally synthesize polycyclic aromatic compounds in nature, and the potential to elaborate further diverse skeletons was recently revealed by the discovery of a polyene subgroup. Here, we show a type II PKS machinery for the biosynthesis of a five-membered nonaromatic skeleton contained in the nonproteinogenic amino acid cispentacin and the plant toxin coronatine. We successfully produce cispentacin in a heterologous host and reconstruct its biosynthesis using seven recombinant proteins in vitro. Biochemical analyses of each protein reveal the unique enzymatic reactions, indicating that a heterodimer of type II PKS-like enzymes (AmcF-AmcG) catalyzes a single C2 elongation as well as a subsequent cyclization on the acyl carrier protein (AmcB) to form a key intermediate with a five-membered ring. The subsequent reactions, which are catalyzed by a collection of type II PKS-like enzymes, are also peculiar. This work further expands the definition of type II PKS and illuminates an unexplored genetic resource for natural products.

Syntheses of (+)-costic acid and structurally related eudesmane sesquiterpenoids and their biological evaluations as acaricidal agents against Varroa destructor.

Synthesis of (+)-costic acid, isolated from Dittrichia viscosa (L.) W. Greuter as a natural acaricidal sesquiterpenoid, was achieved in 16 steps from (R)-carvone with an overall yield of 4.8%, involving the radical cyclization of selenoester to construct a decalone framework as the key step. Other structurally related natural products, (+)-costal, (+)-costol, and (+)-ß-selinene, were also synthesized. The acaricidal activities of these four natural products and some synthetic intermediates were also evaluated against Varroa destructor. Among them, (+)-costal especially exhibited potent acaricidal activity.

Low-Rank Combinatorial Optimization and Statistical Learning by Spatial Photonic Ising Machine.

The spatial photonic Ising machine (SPIM) [13D. Pierangeli et al., Large-Scale Photonic Ising Machine by Spatial Light Modulation, Phys. Rev. Lett. 122, 213902 (2019).PRLTAO0031-900710.1103/PhysRevLett.122.213902] is a promising optical architecture utilizing spatial light modulation for solving large-scale combinatorial optimization problems efficiently. The primitive version of the SPIM, however, can accommodate Ising problems with only rank-one interaction matrices. In this Letter, we propose a new computing model for the SPIM that can accommodate any Ising problem without changing its optical implementation. The proposed model is particularly efficient for Ising problems with low-rank interaction matrices, such as knapsack problems. Moreover, it acquires the learning ability of Boltzmann machines. We demonstrate that learning, classification, and sampling of the MNIST handwritten digit images are achieved efficiently using the model with low-rank interactions. Thus, the proposed model exhibits higher practical applicability to various problems of combinatorial optimization and statistical learning, without losing the scalability inherent in the SPIM architecture.

Digital spatial profiling of CD4+ T cells in classic Hodgkin lymphoma.

Classic Hodgkin lymphoma (CHL) harbors a small number of Hodgkin-Reed-Sternberg (HRS) cells scattered among numerous lymphocytes. HRS cells are surrounded by distinct CD4+ T cells in a rosette-like manner. These CD4+ T cell rosettes play an important role in the tumor microenvironment (TME) of CHL. To elucidate the interaction between HRS cells and CD4+ T cell rosettes, we completed digital spatial profiling to compare the gene expression profiles of CD4+ T cell rosettes and other CD4+ T cells separated from the HRS cells. Immune checkpoint molecules including OX40, programed cell death-1 (PD-1), and cytotoxic T lymphocyte associated protein 4 (CTLA-4) expression was higher in CD4+ T cell rosettes compared to other CD4+ T cells. Immunohistochemistry confirmed variable PD-1, CTLA-4, and OX40 expression in the CD4+ T cell rosettes. This study introduced a new pathological approach to study the CHL TME, and provided deeper insight into CD4+ T cells in CHL.

New synthesis of (±)-karanone, an important aroma compound in agarwood.

A concise synthesis of (±)-karanone, an important aroma compound of agarwood, was achieved from a commercially available 3-methylcyclohex-2-enol in 3.5% yield in 11 steps. The two contiguous stereocenters at C4 and C5 were constructed via Ireland-Claisen rearrangement. The allylic oxidation at C8 was successfully performed with the mixture of tert-butyl hydroperoxide (TBHP) and CuI. A precursor of ring-closing metathesis to construct a bicyclic dienone was efficiently synthesized from iodoenone by 1,4-addition and nucleophilic substitution of the vinyl group in one pot.

Case-based similar image retrieval for weakly annotated large histopathological images of malignant lymphoma using deep metric learning.

In the present study, we propose a novel case-based similar image retrieval (SIR) method for hematoxylin and eosin (H&E) stained histopathological images of malignant lymphoma. When a whole slide image (WSI) is used as an input query, it is desirable to be able to retrieve similar cases by focusing on image patches in pathologically important regions such as tumor cells. To address this problem, we employ attention-based multiple instance learning, which enables us to focus on tumor-specific regions when the similarity between cases is computed. Moreover, we employ contrastive distance metric learning to incorporate immunohistochemical (IHC) staining patterns as useful supervised information for defining appropriate similarity between heterogeneous malignant lymphoma cases. In the experiment with 249 malignant lymphoma patients, we confirmed that the proposed method exhibited higher evaluation measures than the baseline case-based SIR methods. Furthermore, the subjective evaluation by pathologists revealed that our similarity measure using IHC staining patterns is appropriate for representing the similarity of H&E stained tissue images for malignant lymphoma.

Spatial-photonic Ising machine by space-division multiplexing with physically tunable coefficients of a multi-component model.

This paper proposes a space-division multiplexed spatial-photonic Ising machine (SDM-SPIM) that physically calculates the weighted sum of the Ising Hamiltonians for individual components in a multi-component model. Space-division multiplexing enables tuning a set of weight coefficients as an optical parameter and obtaining the desired Ising Hamiltonian at a time. We solved knapsack problems to verify the system's validity, demonstrating that optical parameters impact the search property. We also investigated a new dynamic coefficient search algorithm to enhance search performance. The SDM-SPIM would physically calculate the Hamiltonian and a part of the optimization with an electronics process.

Complete Biosynthetic Pathway of the Phosphonate Phosphonothrixin: Two Distinct Thiamine Diphosphate-Dependent Enzymes Divide the Work to Form a C-C Bond.

Phosphonates often exhibit biological activities by mimicking the phosphates and carboxylates of biological molecules. The phosphonate phosphonothrixin (PTX), produced by the soil-dwelling bacterium Saccharothrix sp. ST-888, exhibits herbicidal activity. In this study, we propose a complete biosynthetic pathway for PTX by reconstituting its biosynthesis in vitro. Our intensive analysis demonstrated that two dehydrogenases together reduce phosphonopyruvate (PnPy) to 2-hydroxy-3-phosphonopropanoic acid (HPPA) to accelerate the thermodynamically unfavorable rearrangement of phosphoenolpyruvate (PEP) to PnPy. The next four enzymes convert HPPA to (3-hydroxy-2-oxopropyl)phosphonic acid (HOPA). In the final stage of PTX biosynthesis, the "split-gene" transketolase homologue, PtxB5/6, catalyzes the transfer of a two-carbon unit attached to the thiamine diphosphate (TPP) cofactor (provided by the acetohydroxyacid synthase homologue, PtxB7) to HOPA to produce PTX. This study reveals a unique C-C bond formation in which two distinct TPP-dependent enzymes, PtxB5/6 and PtxB7, divide the work to transfer an acetyl group, highlighting an unprecedented biosynthetic strategy for natural products.

Total syntheses of dihydro-ß-agarofuran natural products.

Dihydro-ß-agarofuran (DHßAF) sesquiterpenoids constitute a large family of natural products characterized by a tricyclic architecture comprising trans-decalin and tetrahydrofuran rings, and oxygen functionalities on them. Their pharmacologically and agriculturally important biological properties and intriguing molecular architectures have attracted considerable attention from synthetic organic and medicinal chemists. In 2020, our group achieved a scalable total synthesis of this type of natural product, (-)-isocelorbicol, by developing a highly stereocontrolled protocol, which enabled elaboration to naturally occurring ester derivatives, celafolins B-1, B-2, and B-3. Afterward, the total syntheses of more complex DHßAF sesquiterpenoids, (-)-euonyminol and (-)-euonymine, were reported by 2 research groups via current state-of-the-art methods. This review summarizes the total syntheses of DHßAF natural products from 1979 to 2021.

Quantitative analysis of nonlinear optical input/output of a quantum-dot network based on the echo state property.

The echo state property, which is related to the dynamics of a neural network excited by input driving signals, is one of the well-known fundamental properties of recurrent neural networks. During the echo state, the neural network reveals an internal memory function that enables it to remember past inputs. Due to the echo state property, the neural network will asymptotically update its condition from the initial condition and is expected to exhibit temporally nonlinear input/output. As a physical neural network, we fabricated a quantum-dot network that is driven by sequential optical-pulse inputs and reveals corresponding outputs, by random dispersion of quantum-dots as its components. In the network, the localized optical energy of excited quantum-dots is allowed to transfer to neighboring quantum-dots, and its stagnation time due to multi-step transfers corresponds to the hold time of the echo state of the network. From the experimental results of photon counting of the fluorescence outputs, we observed nonlinear optical input/output of the quantum-dot network due to its echo state property. Its nonlinearity was quantitatively verified by a correlation analysis. As a result, the relation between the nonlinear input/outputs and the individual compositions of the quantum-dot network was clarified.

Synthesis and biological evaluation of cajaninstilbene acid and amorfrutins A-D as cytotoxic agents against human pancreatic carcinoma PANC-1 cells.

A concise synthesis of cajaninstilbene acid was achieved in 7 steps from (E)-3,5-dimethoxystilbene in 8.6% overall yield via the Claisen rearrangement of an aryl reverse-prenyl ether as the key step. Cytotoxic activities against human pancreatic carcinoma PANC-1 cells of cajaninstilbene acid and amorfrutins A-D were also evaluated.

Enantioselective synthesis of 6-methyloctanal and 8-methyldecanal, the characteristic aroma components in yuzu Citrus junos, and the analysis of their enantiomeric compositions in yuzu essential oil.

6-Methyloctanal and 8-methyldecanal are the characteristic aroma components of yuzu Citrus junos. However, their absolute configurations and enantiomeric compositions in yuzu essential oil have not been analyzed. A concise enantioselective synthesis of both aldehydes was successfully carried out to determine their absolute configurations and enantiomeric compositions. Both aldehydes in yuzu essential oil were found to be (S)-form with high enantiomeric excess.

Seven-Step Total Synthesis of Sporothriolide.

An enantioselective total synthesis of sporothriolide, a bioactive furofurandione-type fungal metabolite, has been achieved in a 21% overall yield from a commercially available ß,γ-unsaturated carboxylic acid via seven steps. The key steps of this synthesis include a highly diastereoselective Michael addition of a chiral oxazolidinone derivative to a nitro olefin, the exploitation of an aromatic ring as a masked carboxylic acid functionality, and the base-promoted elimination of nitrous acid to install the α-methylene lactone unit of sporothriolide in the final step.

Structural Analysis of Lipid Hydroperoxides Using Mass Spectrometry with Alkali Metals.

Lipid oxidation is involved in various biological phenomena (e.g., oxylipin generation and oxidative stress). Of oxidized lipid structures, the hydroperoxyl group position of lipid hydroperoxides (LOOHs) is a critical factor in determining their biological roles. Despite such interest, current methods to determine hydroperoxyl group positions possess some drawbacks such as selectivity. While we previously reported mass spectrometric methods using Na+ for the highly selective determination of hydroperoxyl group positions, nothing was known except for the fact that sodiated LOOHs (mainly linoleate) provide specific fragment ions. Thus, this study was aimed to investigate the effects of different alkali metals on the fragmentation of LOOHs, assuming its further application to analysis of other complex LOOHs. From the analysis of PC 16:0/18:2;OOH (phosphatidylcholine) and FA 18:2;OOH (fatty acid), we found that fragmentation pathways and ion intensities largely depend on the binding position and type of alkali metals (i.e., Li+, Hock fragmentation; Na+ and K+, α-cleavage (Na+ > K+); Rb+ and Cs+, no fragmentation). Furthermore, we proved that this method can be applied to determine the hydroperoxyl group position of esterified lipids (e.g., phospholipids and cholesterol esters) as well as polyunsaturated fatty acids (PUFAs) including n-3, n-6, and n-9 FA. We anticipate that the insights described in this study provide additional unique insights to conventional lipid oxidation research.

Homophymamide A, Heterodetic Cyclic Tetrapeptide from a Homophymia sp. Marine Sponge: A Cautionary Note on Configurational Assignment of Peptides That Contain a Ureido Linkage.

A previously unreported heterodetic cyclic peptide, homophymamide A (1), was isolated from a Homophymia sp. marine sponge. The structure of homophymamide A was determined to be a lower homologue of anabaenopeptins by spectroscopic analysis, chemical degradation, and chemical synthesis. Analysis of the acidic hydrolysate showed that the racemization of Lys took place, leading us to pose a cautionary note on the configurational assignment of peptides that contain a ureido bond.

JBIR-155, a Specific Class D ß-Lactamase Inhibitor of Microbial Origin.

We discovered JBIR-155 as a novel specific class D ß-lactamase inhibitor from Streptomyces polymachus SoB100815Hv02. JBIR-155 consists of a 6-oxabicyclo[3.2.0]heptan-7-one skeleton and a long unsaturated alkyl chain moiety of which absolute configuration was determined by spectroscopic data, modified Mosher's method, and analyses of the relative configuration of chemically modified derivative. JBIR-155 specifically exhibited inhibitory activity against the class D ß-lactamase, with an IC50 value of 0.36 µM.

Synthesis of a plasmenylethanolamine.

A concise synthesis of a plasmenylethanolamine (PlsEtn-[16:0/18:1 n-9]), known as antioxidative phospholipids commonly found in cell membranes, has been achieved from an optically active known diol through 8 steps. The key transformations for the synthesis of PlsEtn-[16:0/18:1 n-9] are (1) regio- and Z-selective vinyl ether formation via the alkylation of a lithioalkoxy allyl intermediate with an alkyl iodide, and (2) a one-pot phosphite esterification-oxidation sequence to construct the ethanolamine phosphonate moiety in the presence of the vinyl ether functionality. The piperidine salt of synthetic PlsEtn-[16:0/18:1 n-9] was desalinated through reversed-phase high-performance liquid chromatography purification.

Concise enantioselective synthesis of wine lactone via intramolecular Diels-Alder reaction.

An enantioselective synthesis of (3S,3aS,7aR)-wine lactone, a major aroma component of white wine and citrus juices, was achieved starting from (S)-2-methyl-3-butenoic acid. An intramolecular Diels-Alder reaction was employed as a key step.

Unified synthesis and assessment of tumor cell migration inhibitory activity of optically active UTKO1, originally designed moverastin analog.

UTKO1 is a synthetic analog of a natural tumor cell migration inhibitor, moverastin, isolated from microbial extracts of Aspergillus sp. 7720. UTKO1 was initially developed as a mixture of the stereoisomers. In this study, a concise and unified synthesis of the 4 optically active stereoisomers of UTKO1 was achieved from a known optically pure dihydro-α-ionone through a 5-step sequence. The key transformation in the synthesis was a Nozaki-Hiyama-Kishi (NHK) reaction between an optically active enoltriflate and a known aldehyde to install the chiral allylic hydroxy group at C2'. Simple chromatographic separation of the 2 diastereomers with regard to the allylic hydroxy group was possible by the derivatization into the corresponding acetals with Nemoto's optical resolution reagent, (S)- or (R)-5-allyl-2-oxabicyclo[3.3.0]octene (ALBO). All 4 synthetic stereoisomers of UTKO1 exhibited comparable tumor cell migration inhibitory activity.